add_quality_cols: Adds columns 'pep_n_psm', 'prot_n_psm' and 'prot_n_pep'.

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Adds columns pep_n_psm, prot_n_psm and prot_n_pep.

Description

Adds columns pep_n_psm, prot_n_psm and prot_n_pep.

Usage

add_quality_cols(
  df = NULL,
  group_psm_by = "pep_seq",
  group_pep_by = "prot_acc",
  uniq_by = NULL
)

Arguments

df	A data frame.
group_psm_by	A character string specifying the method in PSM grouping. At the pep_seq default, descriptive statistics will be calculated based on the same pep_seq groups. At the pep_seq_mod alternative, peptides with different variable modifications will be treated as different species and descriptive statistics will be calculated based on the same pep_seq_mod groups.
group_pep_by	A character string specifying the method in peptide grouping. At the prot_acc default, descriptive statistics will be calculated based on the same prot_acc groups. At the gene alternative, proteins with the same gene name but different accession numbers will be treated as one group.
uniq_by	A vector of column keys in df defining the levels of uniqueness in PSM entries.

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.